Analyze reticulate evolutionary relationships with this application. PhyloNet is aimed mainly at providing a suite of tools for reconstructing and analyzing reticulate (non-treelike) evolutionary relationships. In particular, the program package includes features for inferring horizontal gene transfer from a pair of species/gene trees, and detecting interspecific recombination breakpoints in a sequence alignment. Further, it has the abilities for reading/storing phylogenetic networks, and comparing phylogenetic networks topologies. As the algorithms for phylogenetic network reconstruction and evaluation make use of algorithmic techniques from the domain of phylogenetic trees, the package also contains several tree-oriented features, such as modules for computing the maximum agreement subtrees, the Robinson-Foulds distance measures, etc.

PhyloNet Features:
1. MAST - Maximum Agreement Subtree
2. RF - Robinson-Foulds/Symmetric Difference tree measure
3. RIATAHGT - a heuristic for detecting HGT events from a pair of species/gene trees
4. LCA - least common ancestor of a set of nodes in a tree
5. RECOMP - a window-based method for detecting interspecific recombination breakpoints
6. CHARNET - a software for computing clusters, trees and tripartitions in a network
7. CMPNETS - a software for computing the distance between two networks
8. NETPARS - a software for scoring the parsimony of phylogenetic networks
9. COUNTCOAL - a software for enumerating all valid coalescent scenarios of a gene within the branches of a species tree
10. GENCPLEX - a software for generating an MILP formulation that can be solved by CPLEX for a species trees and a set of gene trees
11. GENST - a software for generating species tree topoloties based on maximal sets of compatible clusters.
12. COMPUTE_ST (this tool is a Perl script) - for reconstructing the species tree from gene trees under the coalescent.
13. INFER_ST - for inferring the species tree from gene trees. Methods contained include MDC, MDC with time, GLASS, extended Majority Consensus and Democratic Vote.
14. DEEP_COAL__COUNT - for counting the number of extra lineages contributed by a set of gene trees and species trees
15. SIM_GTINNETWORK - for simulating gene trees under the phylogenetic network model in the Yu et al. Syst Biol 2010 paper

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.